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[Rioual <question679320@xxxxxxxxxxxxxxxxxxxxx>]

Question #679320 on Yade changed:
https://answers.launchpad.net/yade/+question/679320

    Status: Answered => Open

Rioual is still having a problem:
Hello Bruno

Thank's for your input.

1- I tried the simulation with different smaller time scales 1e-4, 1e-5, 1e-6 and the error messages appear at fairly the same simulation time apparently:
"
CHOLMOD warning: matrix not positive definite
something went wrong in Cholesky factorization, use LDLt as fallback this time
65 : Vh==NULL!! id=65 Point=-0.803797 -0.683743 1.61915 rad=0.0666365
147 : Vh==NULL!! id=147 Point=-0.927542 -0.647778 1.92058 rad=0.0638237
...etc"

2- Before the error messages, the compression is processed as can be
observed on the graphical output (motion of the boundaries) but nothing
changes when I print the position of the upper plate and the force on
this plate. See a minimal working example code of the compression
process below that shows both problems 1 and 2:

****************************************************************************

## ______________   First section, similar to triax-tutorial/script-session1.py  _________________
from yade import pack

num_spheres=1000# number of spheres
young=1e6
C=1e6
compFricDegree = 3 # initial contact friction during the confining phase
finalFricDegree = 11 # contact friction during the deviatoric loading (for ice!!)
mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing

O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
sp.toSimulation(material='spheres')

triax=TriaxialStressController(
	maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
	finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
	thickness = 0,
	stressMask = 7,
	max_vel = 0.005,
	internalCompaction=True, # If true the confining pressure is generated by growing particles
)

newton=NewtonIntegrator(damping=0.2)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
	),
	FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
	triax,
	newton
]

triax.goal1=triax.goal2=triax.goal3=-10000

while 1:
  print '***' 
  O.run(1000, True)
  unb=unbalancedForce()
  if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
    break

setContactFriction(radians(finalFricDegree))

##Second section: Activate flow engine and set boundary conditions for
the compression (squashing) test, impermeable on each face:

flow.dead=0
flow.defTolerance=0.3
flow.meshUpdateInterval=200
flow.useSolver=3
flow.permeabilityFactor=1
flow.viscosity=10
flow.boundaryUseMaxMin=[0,0,0,0,0,0]
O.dt=1e-4
O.dynDt=False

flow.bndCondIsPressure=[False,False,False,False,False,False]
#flow.bndCondValue=[0,0,0,0,0,0]

newton.damping=0

#aditional compressibility of the fluid
flow.fluidBulkModulus=1e6

triax.stressMask=5
triax.internalCompaction=False
triax.goal2=-0.1
triax.goal1= 0
triax.goal3= 0
triax.wall_left_activated= True
triax.wall_right_activated= True
triax.wall_front_activated= True
triax.wall_back_activated= True
triax.wall_top_activated= True

global plate
plate = O.bodies[triax.wall_top_id]

Ftot0 = O.forces.f(plate.id)[0]
Ftot1 = O.forces.f(plate.id)[1]
Ftot2 = O.forces.f(plate.id)[2]

xtot = plate.state.pos[0]
ytot = plate.state.pos[1]
ztot = plate.state.pos[2]


## a function printing variables
def history():	
	print 't=', O.time, 'Force on the plate (Ftot)=', Ftot0, Ftot1, Ftot2
	print 't=', O.time, 'Position of the plate (xtot,ytot,ztot)=', xtot, ytot, ztot

O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')]

from yade import timing
print "starting squashing simulation"
O.run(200,1)
timing.stats()

************************************************************************************************


Best wishes,

Fr.

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